Light microscopy can be done quickly, but accuracy depends on the experience of the microscopist and quality of equipment. Regulations often limit physicians’ use of microscopy for diagnostic purposes outside a certified laboratory.
Microscopic examination of tissue may be required to distinguish invasive disease from surface colonization—a distinction not easily achieved by culture methods.
Most specimens are treated with stains that color pathogens, causing them to stand out from the background, although of unstained samples can be used to detect fungi and certain other pathogens.
The clinician orders a stain based on the likely pathogens. However, no stain is 100% specific (ie, different organisms may stain similarly). Most samples are treated with and, if mycobacteria are suspected, with an . However, some pathogens are not easily visible using these stains; if these pathogens are suspected, different stains or other identification methods are required.
Because microscopic detection usually requires a microbe concentration of at least about 1 ×104-5/mL, most body fluid specimens (eg, cerebrospinal fluid) are concentrated (eg, by centrifugation) before examination.
Gram stain
The Gram stain does the following:
Classifies bacteria according to whether they retain crystal violet stain (gram-positive—blue) or not (gram-negative—red)
Highlights cell morphology (eg, bacilli, cocci) and cell arrangement (eg, clumps, chains, diploids)
Identifies polymorphonuclear leukocytes, indicating bacterial infection rather than colonization
Such characteristics can direct antibiotic therapy pending definitive identification. Finding a mixture of microorganisms with multiple morphologies and staining characteristics on Gram stain suggests a contaminated specimen or a polymicrobial bacterial infection. Finding many squamous cells in a sputum specimen suggests that the specimen is contaminated with saliva and thus is of limited diagnostic usefulness.
To do a Gram stain, technicians heat-fix specimen material to a slide and stain it by sequential exposure to Gram crystal violet, iodine, decolorizer, and counterstain (typically safranin).
Acid-fast and modified acid-fast stains
These stains are used to identify the following:
Acid-fast organisms (Mycobacterium Tuberculosis (TB) Tuberculosis is a chronic, progressive mycobacterial infection, often with an asymptomatic latent period following initial infection. Tuberculosis most commonly affects the lungs. Symptoms include... read more
species)Moderately acid-fast organisms (primarily Nocardia Nocardiosis Nocardiosis is an acute or chronic, often disseminated, suppurative or granulomatous infection caused by various aerobic soil saprophytes of the gram-positive bacilli genus Nocardia.... read more
species)Rhodococcus and related genera
Oocysts of some parasites (eg, Cryptosporidium Cryptosporidiosis Cryptosporidiosis is infection with the protozoan Cryptosporidium. The primary symptom is watery diarrhea, often with other signs of gastrointestinal distress. Illness is typically self-limited... read more
, microsporidia Microsporidiosis Microsporidiosis is infection with microsporidia. Symptomatic disease develops predominantly in patients with AIDS and includes chronic diarrhea, disseminated infection, and corneal disease... read more , Cystoisospora [Isospora] belli Cyclosporiasis Cyclosporiasis is infection with the protozoan Cyclospora cayetanensis. Symptoms include watery diarrhea with gastrointestinal and systemic symptoms. Diagnosis is by detection of characteristic... read more, Cyclospora Cyclosporiasis Cyclosporiasis is infection with the protozoan Cyclospora cayetanensis. Symptoms include watery diarrhea with gastrointestinal and systemic symptoms. Diagnosis is by detection of characteristic... read more, Balantidium coli)
Although detection of mycobacteria in sputum requires at least 10,000 organisms/mL, mycobacteria are often present in lower levels, so sensitivity is limited. Usually, several mL of sputum are decontaminated with sodium hydroxide and concentrated by centrifugation for acid-fast staining. Specificity is better, although some moderately acid-fast organisms are difficult to distinguish from mycobacteria.
Fluorescent stains
Fluorescent stains allow detection at lower concentrations (< 1 × 104 cells/mL). Examples are
Acridine orange (bacteria and fungi)
Auramine-rhodamine and auramine O (mycobacteria)
Calcofluor white (fungi, especially dermatophytes)
Coupling a fluorescent dye to an antibody directed at a pathogen (direct or indirect immunofluorescence) should theoretically increase sensitivity and specificity. However, these tests are difficult to read and interpret, and few (eg, Pneumocystis and Legionella direct fluorescent antibody tests) are commercially available and commonly used.
Wet mounts
Wet mounts of unstained samples can be used to detect the following via darkfield microscopy:
Fungi Overview of Fungal Infections Fungal infections are often classified as either Opportunistic Primary Opportunistic infections are those that develop mainly in immunocompromised hosts. Primary infections can develop in immunocompetent... read more
Parasites Approach to Parasitic Infections Human parasites are organisms that live on or in a person and derive nutrients from that person (its host). There are 3 types of parasites: Single-cell organisms (protozoa, microsporidia) Multicellular... read more (including helminth eggs and larvae)
Vaginal clue cells (present in bacterial vaginosis Bacterial Vaginosis (BV) Bacterial vaginosis is vaginitis due to a complex alteration of vaginal flora in which lactobacilli decrease and anaerobic pathogens overgrow. Symptoms include a gray, thin, fishy-smelling vaginal... read more
)Motile organisms (eg, Trichomonas Trichomoniasis Trichomoniasis is infection of the vagina or male genital tract with Trichomonas vaginalis. It can be asymptomatic or cause urethritis, vaginitis, or occasionally cystitis, epididymitis... read more )
Treponema spirochetes (present in syphilis Syphilis Syphilis is caused by the spirochete Treponema pallidum and is characterized by 3 sequential clinical, symptomatic stages separated by periods of asymptomatic latent infection. Common... read more
)
Visibility of fungi can be increased by applying 10% potassium hydroxide (KOH) to dissolve surrounding tissues and nonfungal organisms.
India ink (colloidal carbon) stain
India ink stain is used to detect mainly Cryptococcus neoformans Cryptococcosis Cryptococcosis is a pulmonary or disseminated infection acquired by inhalation of soil contaminated with the encapsulated yeasts Cryptococcus neoformans or C. gattii. Symptoms... read more
Warthin-Starry stain and Dieterle stain
These silver stains are used to visualize bacteria such as
Spirochetes Bejel, Pinta, and Yaws Bejel, pinta, and yaws (endemic treponematoses) are chronic, tropical, nonvenereal spirochetal infections spread by body contact. Symptoms of bejel are mucous membrane and cutaneous lesions... read more
Helicobacter pylori Helicobacter pylori Infection Helicobacter pylori is a common gastric pathogen that causes gastritis, peptic ulcer disease, gastric adenocarcinoma, and low-grade gastric lymphoma. Infection may be asymptomatic or... read more
Microsporidia Microsporidiosis Microsporidiosis is infection with microsporidia. Symptomatic disease develops predominantly in patients with AIDS and includes chronic diarrhea, disseminated infection, and corneal disease... read more
Bartonella henselae (the cause of cat-scratch disease Cat-Scratch Disease Cat-scratch disease is infection caused by the gram-negative bacterium Bartonella henselae. Symptoms are a local papule and regional lymphadenitis. Diagnosis is clinical and confirmed... read more
)
Wright stain and Giemsa stain
These stains are used for detection of the following:
in blood
in phagocytes and tissue cells
Intracellular inclusions formed by viruses and chlamydia Chlamydia Three species of Chlamydia cause human disease, including sexually transmitted infections and respiratory infections. All are susceptible to macrolides (eg, azithromycin), tetracyclines... read more
Trophozoites of
Some intracellular bacteria
Trichrome stain (Gomori-Wheatley stain) and iron hematoxylin stain
These stains are used to detect intestinal protozoa.
The Gomori-Wheatley stain is used to detect microsporidia. It may miss helminth eggs and larvae and does not reliably identify Cryptosporidium. Fungi and human cells take up the stain.
The iron hematoxylin stain differentially stains cells, cell inclusions, and nuclei. Helminth eggs may stain too dark to permit identification.